Remove dependence on pkg_resources

.github/workflows/test-pip.yml

@@ -30,9 +30,9 @@ jobs:
       # most of the dependencies
       - name: Install dependencies with PIP
         run: |
-          pip install numpy networkx six pytest pytest-cov ase
+          pip install packaging numpy networkx six pytest pytest-cov ase
 
-      # rdkit: PyPi only supplies it for 3.7 and above
+      # rdkit: PyPi only supplies it for 3.7-3.11
       - name: Install rdkit
         if: matrix.python-version != '3.12'
         run: |

devtools/conda-envs/latest.yaml

@@ -29,6 +29,7 @@ dependencies:
   # geomeTRIC base depends
   - numpy
   - networkx
+  - packaging
 
   # Testing
   - pytest

geometric/config/__init__.py

@@ -0,0 +1,3 @@
+# Path to this configuration directory
+import os
+config_dir = os.path.dirname(os.path.abspath(__file__))

geometric/molecule.py

@@ -2,7 +2,6 @@
 from __future__ import division
 from __future__ import print_function
 
-import copy
 import itertools
 import os
 import re
@@ -12,12 +11,11 @@
 from collections import OrderedDict, namedtuple, Counter
 from ctypes import *
 from datetime import date
-from warnings import warn
 
 import numpy as np
 from numpy import sin, cos, arccos
 from numpy.linalg import multi_dot
-from pkg_resources import parse_version
+from packaging.version import parse as parse_version
 
 # For Python 3 compatibility
 try:

geometric/neb.py

@@ -6,7 +6,6 @@
 import numpy as np
 from copy import deepcopy
 from datetime import datetime
-import pkg_resources
 from .info import print_logo, print_citation
 from .prepare import get_molecule_engine
 from .optimize import Optimize
@@ -17,6 +16,7 @@
 from .nifty import flat, row, col, createWorkQueue, getWorkQueue, wq_wait, ang2bohr, bohr2ang, kcal2au, au2kcal, au2evang, logger
 from .molecule import EqualSpacing
 from .errors import NEBStructureError, NEBChainShapeError, NEBChainRespaceError, NEBBandTangentError, NEBBandGradientError
+from .config import config_dir
 
 def print_forces(chain, avgg, maxg):
     """Check average and maximum chain forces and return color coded string"""
@@ -1648,8 +1648,7 @@ def main():
     params = NEBParams(**args)
 
     if args.get('logIni') is None:
-        import geometric.neb
-        logIni = pkg_resources.resource_filename(geometric.neb.__name__, r'config/log.ini')
+        logIni = os.path.join(config_dir, 'logJson.ini')
     else:
         logIni = args.get('logIni')
 

geometric/normal_modes.py

@@ -836,9 +836,9 @@ def wigner_sample(coords, mass, elem, freqs_wavenumber, normal_modes, temperatur
         print("Wigner distribution sample generation: %s samples %s" % (commadash(ovr_idx), 'overwritten' if overwrite else 'skipped'))
 
 def main(): # pragma: no cover
-    import logging.config, pkg_resources
-    import geometric.optimize
-    logIni = pkg_resources.resource_filename(geometric.optimize.__name__, 'config/logTest.ini')
+    from geometric.config import config_dir
+    import logging.config
+    logIni = os.path.join(config_dir, 'logTest.ini')
     logging.config.fileConfig(logIni,disable_existing_loggers=False)
     M = Molecule("start.xyz")
     coords = M.xyzs[0] / bohr2ang

geometric/optimize.py

@@ -39,14 +39,12 @@
 import sys
 import time
 import traceback
-import pkg_resources
 from copy import deepcopy
 from datetime import datetime
 
 import numpy as np
 from numpy.linalg import multi_dot
 
-import geometric
 from .info import print_logo, print_citation
 from .internal import CartesianCoordinates, PrimitiveInternalCoordinates, DelocalizedInternalCoordinates
 from .ic_tools import check_internal_grad, check_internal_hess, write_displacements
@@ -56,6 +54,7 @@
 from .params import OptParams, parse_optimizer_args
 from .nifty import row, col, flat, bohr2ang, ang2bohr, logger, bak, createWorkQueue, destroyWorkQueue, printcool_dictionary
 from .errors import InputError, HessianExit, EngineError, GeomOptNotConvergedError, GeomOptStructureError, LinearTorsionError
+from .config import config_dir
 
 class Optimizer(object):
     def __init__(self, coords, molecule, IC, engine, dirname, params, print_info=True):
@@ -829,8 +828,7 @@ def run_optimizer(**kwargs):
     # This behavior may be changed by editing the log.ini file.
     # Output will only be written to log files after the 'logConfig' line is called!
     if kwargs.get('logIni') is None:
-        import geometric.optimize
-        logIni = pkg_resources.resource_filename(geometric.optimize.__name__, r'config/log.ini')
+        logIni = os.path.join(config_dir, 'logJson.ini')
     else:
         logIni = kwargs.get('logIni')
     logfilename = kwargs.get('prefix')

geometric/run_json.py

@@ -35,11 +35,11 @@
 
 #!/usr/bin/env python
 
+import os
 import copy
 import geometric
 import json
 import traceback
-import pkg_resources
 import tempfile
 import numpy as np
 
@@ -48,8 +48,8 @@
 except ImportError:
     from io import StringIO
 
-import logging
 from .nifty import logger, RawStreamHandler, commadash
+from geometric.config import config_dir
 
 
 def parse_input_json_dict(in_json_dict):
@@ -191,7 +191,7 @@ def geometric_run_json(in_json_dict):
     """ Take an input dictionary loaded from json, and return an output dictionary for json """
 
     # Default logger configuration (prevents extra newline from being printed)
-    logIni = pkg_resources.resource_filename(geometric.optimize.__name__, 'config/logJson.ini')
+    logIni = os.path.join(config_dir, 'logJson.ini')
     import logging.config
     logging.config.fileConfig(logIni,disable_existing_loggers=False)
 

geometric/tests/addons.py

@@ -6,8 +6,6 @@
 import geometric
 import pytest
 import os
-import logging.config
-import pkg_resources
 
 
 def _plugin_import(plug):

setup.py

@@ -26,6 +26,7 @@
         'networkx',
         'six',
         'scipy',
+        'packaging',
     ],
     tests_require=[
         'pytest',